MUMmer 3.0 is an open-source genome comparison tool that efficiently handles comparisons of large eukaryotic genomes at varying evolutionary distances. It is the first version of MUMmer to be released as open-source software, allowing other developers to contribute to the code base and freely redistribute the code. The tool includes new graphical viewing tools for analyzing genome alignments and is designed to handle large-scale genome comparisons, including those of closely related and more distantly related species. The system uses a suffix-tree data structure for efficient alignment, which allows for faster and more memory-efficient processing compared to previous versions. MUMmer 3.0 also supports non-unique and non-exact matches, enhancing its flexibility. The tool has been tested on various genome comparisons, including bacterial, fungal, and mammalian genomes, and has shown improved performance over previous versions. The software is available at http://www.tigr.org/software/mummer. MUMmer 3.0 includes new features such as a Java viewer for genome comparisons and the ability to handle multi-contig queries. The tool is also used for evaluating genome assemblies and comparing different genome assemblies. The open-source nature of MUMmer 3.0 encourages further development and improvement by the scientific community.MUMmer 3.0 is an open-source genome comparison tool that efficiently handles comparisons of large eukaryotic genomes at varying evolutionary distances. It is the first version of MUMmer to be released as open-source software, allowing other developers to contribute to the code base and freely redistribute the code. The tool includes new graphical viewing tools for analyzing genome alignments and is designed to handle large-scale genome comparisons, including those of closely related and more distantly related species. The system uses a suffix-tree data structure for efficient alignment, which allows for faster and more memory-efficient processing compared to previous versions. MUMmer 3.0 also supports non-unique and non-exact matches, enhancing its flexibility. The tool has been tested on various genome comparisons, including bacterial, fungal, and mammalian genomes, and has shown improved performance over previous versions. The software is available at http://www.tigr.org/software/mummer. MUMmer 3.0 includes new features such as a Java viewer for genome comparisons and the ability to handle multi-contig queries. The tool is also used for evaluating genome assemblies and comparing different genome assemblies. The open-source nature of MUMmer 3.0 encourages further development and improvement by the scientific community.